Why do I get
the message "ERROR: Blast: No valid letters to be
indexed"?

You may have accidentally entered an accession number in
the search box without changing the input selection from
"Sequence in FASTA format" to "Accession or gi". You will
also see this error message if too many ambiguity codes
(R,Y,K,W,N, etc. fornucleotides) are present in your query
sequence. Although BLAST allows ambiguity codes, be aware
that these will always contribute a negative score in
nucleic acid searches. Thus, sequences such as degenerate
PCR primers with ambiguity codes maynot find any
significant hits even though they may be designed from
sequences that are present in the database.